"Officially, Starfleet is subordinate to the civilian government. But unofficially, Starfleet restricts [security] clearance so that no one in the civilian government need be made aware of our actions, not even the President," said one high-ranking member of Starfleet who asked not to be identified. Government critics have long charged that Starfleet is effectively a "shadow government", making policy decisions and even using its own officers in foreign policy negotiations, with or without the input or approval of the civilian government.
When they mentioned Contagion I thought there was going to be something about the computer science and the fact that they spend the entire episode trying to come up with a solution that pretty much everybody with a computer knows how to do nowadays.
One thing I want to point out that might count as a defense against some of their criticisms. The warp core is one issue, and the point about using overly complicated technology (why is the transporter capable of turning them into children?), and the point about their hilariously unsafe testing procedures. But with the who redundancy/isolation/diversity thing, it's not true that they don't have redundancy. They have massive amounts of redundancy, and they've given up diversity and isolation to achieve it. They're always rerouting resources from any given system to fix any other given system. The redundancy complaint about the phasers overlooks this, I think because the reallocation is always manual. You could argue that it has to be manual because all the systems can reroute their resources to each other and you need a human making decisions to juggle this appropriately. Apparently they've decided that integrating their systems and homogenizing their technology will solve more problems that it creates, so they've maximized redundancy at the expense of the other two principles. All their technology can be used to fix all their other technology (even getting beyond the ship itself you see this all the time) and as a result they've sacrificed the principal of isolation.